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DRIMM (Drifting Markov Models)

DRIMM is a software dedicated to the estimation of Drifting Markov Models (see [1] and [2]). See a more detailed description at this page.

[1] Vergne, N. Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences. Statistical Applications in Genetics Molecular Biology 2008, vol 7, issue 1.
[2] Vergne, N. Chaînes de Markov régulées pour l'analyse de séquences biologiques. PhD thesis, Université d'Evry val d'Essonne, 2008.

DRIMM provides four programs :

1. DRIMM : Estimation of DMM by different methods.
2. PVALUEdmm : Compute the p-value of a word under a DMM. This program needs a configuration file generated by DRIMM and a markov file generated by Spatt (*).
3. PROBAword : Compute, at each position in the sequence, the probability that a word appears. This program needs a configuration file generated by DRIMM.
4. PROBAlength : Compute, at each position, the probability of appearance of the word of size length who appears in this position. This program needs a configuration file generated by DRIMM.

(*) http://stat.genopole.cnrs.fr/spatt/

How to have DRIMM in your home?

DRIMM is written in ANSI C++ and developed on x86 GNU/Linux systems with GCC 3.4, and successfully tested with GCC latest versions on Sun and Apple Mac OSX systems. It relies on seq++ library. Compilation and installation are compliant with the GNU standard procedure. DRIMM is licensed under the GNU General Public License (GNU GPL).

You have to download seq++ before downloading DRIMM.

1. Download seq++
2. Download DRIMM

Help for use of the four programs is provided:

1. DRIMM
2. PVALUEdmm
3. PROBAword
4. PROBAlength